I tend to prefer a smaller number of broader skills in my games. To that end, I consolidated and merged a few skills in my DF game.
This isn't my "dream merge" list - if I was doing a game from scratch, I might tighten the list further. But I want to be able to use other people's stuff easily, and pre-published stuff easily, so big changes are out.
Filch - I've merged that with Pickpocket, as discussed here.
Connoisseur (Weapons) - Merged its function of evaluating price into Armoury (Melee Weapons) and (Missile Weapons.) I'm with Mark Langsdorf on this one - it's very narrow and really, I'm fine with "It's Dwarven and it's worth 400!" being one skill.
Main-Gauche - Eliminated in favor of Knife. If you want to fight off-hand with a Knife, learn Knife. But what about the fencing parry bonus? If the weapon has a F on it, you get it. Otherwise, no.
Physiology (Monster type) and Psychology (Monster type) - Merged with the appropriate Hidden Lore specialty. My main goal with skills like these is to allow people to make rolls to see if they know how to do X to creature Y, or answer the question "What does this character know about these creatures?" They can make it about physiology ("Do I know where its vitals are?") or psychology ("Do demons want money or souls or what?") if they want. This one is recent, I realized I don't want them after this person asked about them. This also has the nice effect of making the base templates that use them better at this kind of stuff, without making everyone else by default unable to target the vitals of strange monsters.
Shield (Buckler) - All shields are covered with Shield, not split into Shield and Shield (Buckler). Bucklers are just harder to hold on to and worse in slams and bashes, but faster to ready. Both get one skill.
Smuggling - merged into Holdout, again, discussed here. DF is not a game that really needs both. Good at one means good at both, I'm fine with that.
Some skills just got nixed as useless in my game:
Hiking - This is one that would be useful in a wilderness game with real time constraints/resource restraints. In my megadungeon game, it's useless, so I give the points back to the guys who have it on their template - Scout and Barbarian, for example. Why charge them for things I'm not going to make them roll?
Shadowing - in my dungeon-based DF game, this is useless. So I just use it off its Stealth default (Stealth-4 on foot) and leave it at that.
I'm still debating merged Strategy and Tactics, as an unnecessary over-specialization of skills in a game that's rarely about leading troops. But I haven't yet, because I'm not sure I want to make that leap quite yet - especially since it would mean Wizards potentially are great at aiding buddies in tactical combat (Strategy is a Background Skill for that template.) But it's on the table.
As you can see, I haven't gone nuts. But I've narrowed down the skills that cover similar ground a little bit. These are few enough that I can easily use pre-made characters with little problem (dump a skill here, put the points there). Bigger changes would mean less portability of the characters, too.
Why not just use Wildcard skills, you might ask? Simple. I don't want that loose of a feel to my game. I don't want Knights and Thieves and Barbarians to have all of their skills identical, all covered by Knight! or Thief! or Barbarian! That's not the feel I want, I just want a slightly narrowed list of things to buy, track, and use.